tbuckley/cabot-search huggingface dataset:
RARE-02. OBSERVATIONAL REGISTRY STUDY OF TREATMENT PRACTICES AND LONG-TERM OUTCOMES OF CHILDREN WITH NEUROFIBROMATOSIS TYPE 1 (NF1) AND PLEXIFORM NEUROFIBROMAS (PN) INITIATING SELUMETINIB IN REAL-WORLD PRACTICE IN THE UNITED STATES (US): STUDY DESIGN AND METHODOLOGY
Authors: Angela Waanders, Kaleb Yohay, Shona Fang, Svea Wahlstrom, Miriam Bornhorst, Julia Meade, Kelly Vallance, Randolph de la Rosa Rodriguez
Journal: Neuro-Oncology (2023)

Abstract Selumetinib (ARRY-142886, AZD6244) is an oral, allosteric MEK1/2 inhibitor approved in the US for children aged ≥2 years with NF1 and symptomatic, inoperable PN, based on results from the pivotal SPRINT study. Aims of the US Selumetinib Registry study [NCT05683678] include understanding treatment practices and assessing short- and long-term safety and effectiveness outcomes of selumetinib treatment in children with NF1-PN in real-world US practice. Clinical and non-clinical factors affecting outcomes will also be explored. This observational registry study of pediatric patients with NF1-PN will be conducted in up to 22 US centers. Eligible patients will be 2–18 years old at the time of selumetinib initiation (on/after April 10, 2020), and not currently participating in a clinical trial. Patients will be divided into three cohorts: Cohort 1 – treatment discontinued before enrollment, Cohort 2 – treatment initiated before enrollment and currently on treatment, Cohort 3 – treatment initiation intended within 3 months of enrollment. Patients will be followed for ≥36 and up to 60 months. Primary objectives are to describe patient demographics and disease characteristics (including diagnosis criteria and related manifestations, diagnostic tests and results, and PN-related morbidities), selumetinib treatment course, short- and long-term effectiveness and safety, and disease course and treatment following discontinuation. Key secondary objectives include measures of quality of life, pain and physical functioning before, during, and after selumetinib. Target enrollment is 200 patients with a 24-month enrollment period and will begin in 2023. The US Registry study will facilitate understanding of treatment practices and assess short and long-term outcomes of selumetinib for NF1-PN in a real-world setting.
TRLS-03. IBRUTINIB DISRUPTS BLOOD-TUMOR BARRIER INTEGRITY TO ENHANCE CNS DRUG DELIVERY AND RODENT GLIOMA MODEL SURVIVAL
Authors: Sanghee Lim, Minhye Kwak, Kayen Tang, Melissa Cesaire, Robert Robey, Michael Gottesman, Sadhana Jackson
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND In the setting of malignant glioma, cytotoxic drugs are often inhibited from accessing the tumor site due to the blood-brain-barrier (BBB). Identifying agents that transiently increase BBB permeability would advance glioma treatment. Ibrutinib, an FDA approved lymphoma treatment, has previously impaired aortic endothelial adhesion and in combination with cytotoxic therapy, increased rodent glioma model survival. In this study, we propose ibrutinib inhibits brain endothelial cell junctional expression to disrupt BBB integrity and increase chemotherapy delivery to malignant glioma cells. METHODS Using rat glioma cells, S635, we evaluated treatment effects with doxil (3mg/kg), ibrutinib (25mg/kg) and combination therapy. We measured effects with serial brain MRIs, doxil plasma and brain regional concentrations, along with 3kD dextran permeability. To evaluate the effects of ibrutinib on in vitro brain endothelial cells, we measured changes in cell-cell electrical impedance and rhodamine efflux, as a surrogate of Abcb1 transporter function, over time (0 to 8h) and at varied drug concentrations (1, 5, and 10µM ibrutinib). RESULTS Ibrutinib in combination with doxil, prolonged median survival in rodent glioma models (18 vs. 24days, p&amp;lt;0.05). MRI findings demonstrated a -14 or -53% vs -75% tumor volume change with doxil or ibrutinib alone vs. combination therapy, respectively (p&amp;lt;0.05). Comparing combination therapy vs. doxil alone, ibrutinib increased CNS concentrations of doxil in the tumor injected brain regions with statistical significance (56ng/mL vs. 74.6ng/mL, p&amp;lt;0.05). In in vitro studies, ibrutinib decreased brain endothelial cell-cell impedance maximally at 2 hours, in a dose dependently without affecting cell viability. Additionally, we observed ibrutinib dose dependently inhibit Abcb1 activity in both endothelial and glioma cells. CONCLUSION Our results suggest ibrutinib increases brain endothelial permeability by causing junctional disruption and inhibition of Abcb1, resulting in increased CNS drug entry and prolonged survival in glioma rat models.
DIPG-07. ROBUST CGAS-STING PATHWAY MEDIATED-INDUCTION OF ANTITUMOR ADAPTIVE IMMUNE RESPONSE: A POTENTIAL FOR DMG IMMUNOTHERAPY
Authors: Banlanjo Umaru, Deepak Mishra, Shiva Senthil Kumar, Brendan Devine, Rachid Drissi
Journal: Neuro-Oncology (2023)

Abstract Immunotherapy has emerged as groundbreaking in cancer treatment showing improved overall survival of patients with advanced cancers. However, its application for diffuse midline glioma (DMG) is still challenging due to the non-inflammatory immune environment with lack of T lymphocyte infiltration, low mutation burden associated with low or absence of neo-antigen expression and suppressive immune microenvironment in DMG. Therefore, determination of novel factors that not only trigger the immune response but also evading the tumor immunosuppression is imperative. The cGAS-STING pathway was shown to elicit the maturation and activation of dendritic cells (DCs) in response to the release of double stranded DNA (dsDNA) from tumor cells leading to effective cytotoxic T-cell infiltration and activity. Here, we aimed to determine the effects of a small molecule PTC596 (BMI-1 modulator and tubulin biding molecule) in cGAS-STING pathway activation and induction of antitumor immunity. We have previously reported the single agent efficacy for PTC596 in controlling tumor growth and improving survival compared to vehicle-treated mice. Our preliminary results using PTC596, indicate the presence of multinucleated cells and the formation of micronuclei, colocalizing with cGAS and induction of STAT1 activation (marker of inflammation through type 1 IFN). We are currently evaluating purified DCs post-PTC596 treatment for the activation of the cGAS-STING pathway and interferon-stimulated genes (ISGs) and determining their cross-priming capacity. In vivo, using our established syngeneic orthotopic DIPG models, we are evaluating the T cell infiltration (CD3, CD4 and CD8), and characterizing the tumor microenvironment in response to PTC596. Data collected from the above experiments will be presented and discussed.
Tracking Targets of Dynamic Super-Enhancers <i>in Vitro</i> to Better Characterize Osteoclastogenesis and to Evaluate the Effect of Diuron on the Maturation of Human Bone Cells
Authors: Robel A. Tesfaye, Melanie Lavaud, Céline Charrier, Bénédicte Brounais-Le Royer, Pierre-François Cartron, Franck Verrecchia, Marc Baud’huin, François Lamoureux, Steven Georges, Benjamin Ory
Journal: Environmental Health Perspectives (2023)

Background: Osteoclasts are major actors in the maintenance of bone homeostasis. The full functional maturation of osteoclasts from monocyte lineage cells is essential for the degradation of old/damaged bone matrix. Diuron is one of the most frequently encountered herbicides, particularly in water sources. However, despite a reported delayed ossification in vivo, its impact on bone cells remains largely unknown. Objectives: The objectives of this study were to first better characterize osteoclastogenesis by identifying genes that drive the differentiation of CD14+ monocyte progenitors into osteoclasts and to evaluate the toxicity of diuron on osteoblastic and osteoclastic differentiation in vitro. Methods: We performed chromatin immunoprecipitation (ChIP) against H3K27ac followed by ChIP-sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) at different stages of differentiation of CD14+ monocytes into active osteoclasts. Differentially activated super-enhancers and their potential target genes were identified. Then to evaluate the toxicity of diuron on osteoblasts and osteoclasts, we performed RNA-Seq and functional tests during in vitro osteoblastic and osteoclastic differentiation by exposing cells to different concentrations of diuron. Results: The combinatorial study of the epigenetic and transcriptional remodeling taking place during differentiation has revealed a very dynamic epigenetic profile that supports the expression of genes vital for osteoclast differentiation and function. In total, we identified 122 genes induced by dynamic super-enhancers at late days. Our data suggest that high concentration of diuron (50μM) affects viability of mesenchymal stem cells (MSCs) in vitro associated with a decrease of bone mineralization. At a lower concentration (1μM), an inhibitory effect was observed in vitro on the number of osteoclasts derived from CD14+ monocytes without affecting cell viability. Among the diuron-affected genes, our analysis suggests a significant enrichment of genes targeted by pro-differentiation super-enhancers, with an odds ratio of 5.12 (ρ=2.59×10−5). Discussion: Exposure to high concentrations of diuron decreased the viability of MSCs and could therefore affect osteoblastic differentiation and bone mineralization. This pesticide also disrupted osteoclasts maturation by impairing the expression of cell-identity determining genes. Indeed, at sublethal concentrations, differences in the expression of these key genes were mild during the course of in vitro osteoclast differentiation. Taken together our results suggest that high exposure levels of diuron could have an effect on bone homeostasis. https://doi.org/10.1289/EHP11690
IMMU-11. PRECLINICAL HIGH-RISK PEDIATRIC BRAIN TUMOR MODELS FOR IMMUNOTHERAPY: HURDLES AND THE WAY FORWARD
Authors: Deepak Mishra, Shelli Morris, Dean Popovsk, Andrew Bondoc, Shiva Senthil Kumar, James Rutka, Annie Huang, Jim Olson, Maryam Fouladi, Rachid Drissi
Journal: Neuro-Oncology (2023)

Abstract Despite recent therapeutic advancements in the treatment of pediatric brain tumors, high-risk brain tumors (pHRBT) remain the leading cause of cancer-related deaths in children. In recent years, immunotherapy has become a viable treatment option for several cancers including brain tumors. However, several factors have limited the use of immunotherapy in the treatment of pHRBT. For example, an "immunologically cold" tumor environment has been predominantly implicated in the failure of checkpoint inhibitors (ICIs) as monotherapy in pHRBT. Nevertheless, priming the effects of ICIs with epigenetic modulators through a process called “viral mimicry” that induces the expression of human endogenous retroviruses has the potential to enhance immunotherapy by sparking a T-cell mediated immune response. However, the inadequate understanding of the limitations of the preclinical models has prevented the development of efficient immunotherapy strategies for pHRBT. Although several studies and reviews have compiled some limitations of the available models, a hands-on experience using preclinical models for ICIs testing has not been fully communicated. Here, we share our bedside to bench experience with syngeneic and humanized mouse models of DIPG, ATRT, and medulloblastoma using ICIs therapy in conjunction with an epigenetic alteration. We will present and discuss the limitations of mouse models for the development of immunotherapies for pHRBT. For instance, our results indicated that the baseline levels of MHC-I expression in patients’ DIPG tumors were comparable to matched normal tissue. However, these levels were significantly lower in mouse DIPG tumors. To compensate for this difference, we treated mice with IFN-γ in combination with an epigenetic modulator. Surprisingly, the addition of INF-γ had a negative effect on animal overall survival compared to the treatment with the epigenetic modulator alone. Together, our experience demonstrated the importance of suitability assessment of current models for developing and translating successful immunotherapy strategies to treat pHRBT.
DIPG-17. TREATMENT OF DIFFUSE INTRINSIC PONTINE GLIOMA USING ALLELE-SPECIFIC SIRNA TARGETING H3.3 K27M MUTANT HISTONE
Authors: Simon Wentworth, Ana Rita Batista, Julia Alterman, Anastasia Khvorova, Miguel Sena-Esteves
Journal: Neuro-Oncology (2023)

Abstract In recent years CNS tumors have surpassed leukemia and lymphoma as the deadliest forms of pediatric cancer, yet many of these tumors remain resistant to treatment. Understanding of the molecular pathology of a particularly fatal pediatric glioma, diffuse intrinsic pontine glioma (DIPG), has improved dramatically over the past decade. However, this knowledge has not yet yielded new targeted therapeutics or advances in treatment. The majority of DIPG tumors (~70-80%) harbor a K27M mutation in the histone H3.3 gene resulting in significant epigenetic changes which drive tumorigenesis. We are utilizing cutting edge siRNA chemistries to develop a therapeutic specifically targeting this oncohistone H3.3 K27M. It has been shown by others that ex vivo disruption of the H3.3 K27M mutant significantly delays tumor development in orthotopic xenograft models and could be a promising target for treatment of disease. New siRNA chemistries allow broad distribution and silencing throughout the brain with durable silencing for months. Utilizing this technology, we have engineered siRNA compounds that can discriminate between wild-type (WT) and K27M mutant H3.3 alleles. Our first-generation compounds achieved &amp;gt;95% silencing of K27M mutant with only 40% silencing of WT H3.3. We have developed second-generation compounds to improve the discrimination between the two alleles. These compounds allow us to selectively knockdown the mutant driver of DIPG tumorigenesis and we hypothesize that silencing of this oncohistone will revert the epigenetic landscape of DIPG to a more wild-type form detrimentally impacting tumor growth and progression. Together the in vivo potency of the new siRNA chemistries combined with the precision allele-specific targeting of mutant K27M oncohistone may be a promising path towards development of an effective and safe therapy for DIPG.
MDB-37. CDK9 IS A DRUGGABLE MEDIATOR SUSTAINING MYC-DRIVEN TRANSCRIPTIONAL CIRCUITRY IN MEDULLOBLASTOMA
Authors: Madhavan Krishna, Faye Walker, Lays Martin Sobral, Dong Wang, Bethany Veo, Ilango Balakrishnan, Angela Pierce, Natalie Serkova, Nicholas Foreman, Sujatha Venkataraman, Rajeev Vibhakar, Nathan Dahl
Journal: Neuro-Oncology (2023)

Abstract Though long recognized as a master regulator of cell proliferation across a wide range of cancers, Myc has proven elusive to direct therapeutic targeting. The CDK9-containing PTEFb, complexed with either BRD4 or SEC, facilitates Myc-driven transcriptional programs and is necessary for sustaining expression of Myc itself. Advances in development of clinical-grade CDK9 inhibitors creates an opportunity to examine this as a rational therapy for Myc-driven medulloblastoma (Myc-MB). In order to define the enhancer-promoter circuitry driving Myc expression in medulloblastoma, we performed chromosome conformation capture (Hi-C) from primary patient Myc-MB samples. Using a combination of CUT&amp;RUN and RNA-seq, we find that treatment with the CDK9 inhibitor zotiraciclib depletes Myc binding and transcriptional activity at enhancer elements within the Myc topologically associated domain, largely abrogating transcriptional output from the Myc promoter. This leads to a decrease in Myc binding genome-wide with a concordant downregulation of hallmark Myc-driven transcriptional programs. Myc-MB cell lines are sensitive to CDK9 inhibition at low nanomolar concentrations, with a loss of fitness as measured by decreased proliferative or clonogenic potential and a marked induction of apoptosis. Clinically relevant CDK9 inhibitors show variable efficacy in vivo, but CNS-penetrant agents achieved a significant prolongation in xenograft survival. Together, these data demonstrate that CDK9 catalytic activity represents a druggable vulnerability underpinning Myc-driven transcriptional programs. The development of CNS-penetrant CDK9 inhibitors may open new avenues for rational therapy in these high-risk medulloblastomas.
BIOL-20. BIOPROCESSING OF SURGICAL PEDIATRIC BRAIN TUMOR SPECIMENS FOR GENOME-GUIDED PERSONALIZED DRUG TESTING
Authors: Emon Nasajpour, Caitlynn Tran, Cesar Garcia, Geoff Lyle, Maria I Barros Guinle, Bryce A Bagley, Hope Lancero, Eden E Gibson, Troy Schouten, Kelly Mahaney, Hannes Vogel, Katrina Learned, Olena Vaske, Gerald A Grant, Laura M Prolo, Claudia K Petritsch
Journal: Neuro-Oncology (2023)

Abstract Novel treatment approaches are urgently needed for pediatric central nervous system (CNS) tumors as they are the leading cause of cancer-related deaths in children. A lack of research materials impedes progress towards developing such therapies. Although various brain cancer biobanks exist, these rarely store viable patient-derived tissue and cells for live cell analyses, including cell fate assays and testing for drug sensitivities. We propose that a biorepository of viable cell dissociates and tissue broadly representing CNS tumor entities overcomes these limitations. From a combination of molecular diagnoses and histopathologic assessment of over 90 samples collected, we generated a biorepository of roughly 35 distinct entities of pediatric CNS tumors in our Stanford neuro-bioprocessing cohort. Based on the Central Brain Tumor Registry of the United States, the proportion of subtypes represented in our cohort match that of the general population with exceptions. We established a standardized bioprocessing pipeline that can be used as a template for tissue collection and model development in the broader disease context and for multiple downstream applications. Our emphasis on cryostorage of viable cells and tissue facilitates ad hoc live cell analyses. In addition to gaining a better understanding of tumor pathophysiology, we attempted a rapid bed-to-bench-to-bedside approach using comparative RNA expression profile analyses in an individual patient’s pilocytic astrocytoma. Novel drug targets were identified by analyzing RNA transcripts that are highly expressed (outliers) compared with a compendium of 12,747 brain and non-brain tumor samples. We validated outliers as drug targets using acute cell isolates, and identified a novel target in recurrent low-grade glioma. These studies illustrate that biobanking of viable patient-derived material enables developing personalized therapies with the goal of improving patient outcomes. As demonstrated here, patient-derived acute cell isolates facilitate identifying drug vulnerability, creating an opportunity for more personalized treatment of patients with CNS tumors.
IMG-03. HARNESSING COMPUTATIONAL IMAGING, SCALABLE CLOUD-BASED WORKFLOWS, AND MULTI-MODAL DATA ANALYTICS WITH INTEROPERABLE SOFTWARE PLATFORMS IN PEDIATRIC NEURO-ONCOLOGY; THE ROAD AHEAD FOR CHILDREN’S BRAIN TUMOR NETWORK (CBTN)
Authors: Ali Nabavizadeh, Ariana Familiar, Anahita Fathi Kazerooni, Karthik Viswanathan, Meen Chul Kim, Alex Lubneuski, Allison P Heath, Arastoo Vossough, Phillip B Storm, Adam C Resnick
Journal: Neuro-Oncology (2023)

Abstract Neuroimaging is acquired as part of the clinical standard of care for treatment of brain tumor patients. Capitalizing on this data and integration of imaging with other data types to perform predictive analytics is an increasing need. Here, we review the efforts at CBTN in the past couple of years to establish user-friendly workflows to support the entire imaging data lifecycle and to bridge access to multi-modal datasets with scalable analytics scale, to empower researchers to make breakthrough discoveries that will advance patient care. An automated deep learning-based brain extraction and tumor subregion segmentation model based on a multi-institutional dataset was developed that can reliably segment the MRI scans of children across a variety of brain tumor histologies. This model was subsequently integrated into an end-to-end imaging pipeline for collecting, managing, and analyzing clinically acquired radiology exams of the CBTN consortium with processing of 12,500 exams to date. A public website was also created to allow users to search and explore the dataset based on sequence labels, and clinical and imaging attributes. In addition, we established a scalable workflow and processes for de-identification, ingestion, quality control, and management of digital pathology slides on CBTN (over 8,000 slides to date). Finally, we established interoperability between imaging (Flywheel) and molecular (CAVATICA) platforms deployed in cloud ecosystems which allows streamlined, user-friendly workflows to ingest and harmonize files, perform cohort selection, prepare data using standard processing packages and cloud resources, and conduct analysis on extracted multi-modal feature sets. The described workflow lays the foundation for broad use of imaging studies and access to multi-modal datasets and analytics, with the goal of empowering researchers to make breakthroughs in patient care. The next step is to apply these tools in the context of clinical trials.
MDB-34. “INDUCING IRON IMBALANCE BY TARGETING THE ABCB7/GPX4 AXIS ACCELERATES FERROPTOSIS IN MEDULLOBLASTOMA”
Authors: Ranjana Kanchan, Naveenkumar Perumal, David Doss, Parvez Khan, Ramakanth Venkata, Ishwor Thapa, Raghupathy Vengoji, Jyoti Kaushal, Jawed Siddiqui, Mohd Wasim Nasser, Surinder Batra, Sidharth Mahapatra
Journal: Neuro-Oncology (2023)

Abstract Medulloblastomas (MB), the most common malignant pediatric brain tumor and a leading cause of childhood mortality, are stratified into four primary subgroups. Deletions within chromosomal locus 17p13.3, which houses multiple tumor suppressor genes including miR-1253, characterize high-risk group 3 tumors. These aggressive tumors also enrich iron transport genes to satisfy their high proliferative need. MiR-1253 targets iron transport by inhibiting the mitochondrial Fe-S transporter, ABCB7. This study elucidated the impact of repressing ABCB7 on cisplatin cytotoxicity in group 3 MB and whether these effects were mediated by ferroptosis. In silico and in vitro analyses revealed specific enrichment of ABCB7 and GPX4, a critical regulator of ferroptosis, in group 3 MB cell lines and tumors. MiR-1253 overexpression (miR-1253OE) resulted in downregulation of both ABCB7 and GPX4, concurrently increasing mitochondrial iron overload, mitochondrial oxidative stress, and lipid peroxidation, leading to cell death and abrogation of medullosphere formation; ABCB7 knockdown (ABCB7KD) recapitulated these effects and abrogated GPX4 expression. Fractionation studies confirmed the inhibitory impact of miR-1253OE and ABCB7KD on GPX4 expression in the cytosol and mitochondria. Seahorse studies revealed that the bulk of ATP generation was occurring in the cytoplasm through glycolysis and not via oxidative phosphorylation, suggesting mitochondrial dysfunction was triggered when ABCB7 was repressed. Cisplatin, a chemotherapeutic agent used in group 3 MB treatment, induces cell death by DNA crosslinking; it also inhibits GPX4 expression. In miR-1253OE and ABCB7KD group 3 cancer cells, cisplatin IC50 was reduced 2-fold. Resultantly, cisplatin treatment augmented oxidative stress and lipid peroxidation, depleted glutathione stores, and culminated in a higher index of ferroptosis. In a mouse model of group 3 tumors, ABCB7KD potentiated cisplatin effects and dramatically prolonged survival. The current study illustrates how targeting iron transport can augment ferroptosis to potentiate cisplatin cytotoxicity in group 3 MB tumors.